March 2, 2016

Bioo Scientific Corporation is an Austin, TX based biotechnology company that provides innovative solutions for food and feed safety testing and life science research. The company recently released NextflexTM Custom Amplicon Panels, for Illumina or Ion Torrent-based Next Generation Sequencing. These fully customizable amplicon panels allow researchers to sequence up to 2,000 amplicons using a simple workflow, covering regions as little as 1 kb and as large as 500 kb of the genome. This highly targeted sequencing approach offers unparalleled efficiency for discovering, validating, and screening genetic variants. Custom DNA and RNA panels can be designed for a variety of input materials (fresh or frozen tissue, FFPE, and cell free samples).

In order to deliver Custom Amplicon Panels, Bioo Scientific is using proprietary primer design software (NextflexTM Amplicon StudioTM). Quality primer design is the most critical aspect of PCR based targeted sequencing. NextflexTM Amplicon StudioTM delivers panels with >90% of bases covered at 0.2x of mean coverage and >90% reads on target. Bioo Scientific’s primer design harnesses the power of computation and exploits the relationship between all user-specific arguments. Well-defined primer selection criteria, robustness, and an interactive and flexible design fueled by machine learning allows Bioo Scientific to produce high quality candidate primers for any genomic target.

Challenges Faced Before Moving to the Cloud

Bioo Scientific was running on a workstation, which is very timely in completing target regions. Researchers have access to 24 cores, enabling them to run 21 jobs or targets concurrently. This is adequate when working on only one gene for one panel. However, the challenge researchers face is that panels vary in size. For instance, when trying to work on 21 panels composed of 58 genes, there are 700 targets. Trying to run 700 jobs locally did not make sense, nor was it economical.

The company turned to the ACTnowHPC cloud solution so that the work could be done in parallel, which meant the results are delivered much faster. Cloud computing allows Bioo Scientific to process custom work much more efficiently. After testing several platforms, Bioo Scientific discovered that ACTnowHPC delivers results more quickly due to less queue time and slightly better processing time on a per job basis. Today Bioo Scientific is utilizing the cloud cluster to run NextflexTM Amplicon StudioTM for the mass design of target specific PCR primers.

Benefits of Working in the Cloud

Before the release of custom panels, Bioo Scientific was using the same software to perform much smaller jobs, for fixed panels. For example, the NextflexTM BRCA1 and BRCA2 Amplicon Panel designed for use with FFPE, and cell free samples. This panel was initiated as a fixed product, and designed using local compute capabilities. For only two genes which are very well studied, local compute was logical.

Rather than selecting genes and designing fixed panels to sell, Bioo Scientific’s business strategy is to offer custom products, specific to meet any customer’s sequencing needs. Offering custom products is much more desirable in NGS not only for saving time and cost, but also as a solution for specific research goals. Custom Amplicon Panels allow sequencing of very specific information, giving the researcher exactly what they requested.

Using ACTnowHPC allows Bioo Scientific to accept several custom orders and design high quality primers more efficiently. The cloud reduces time from initial customer contact to product delivery because it allows for much higher throughput of information. The ability to run hundreds of jobs at the same time is really what makes the difference.